MOSTA database has a total of 53 sagittal sections from C57BL/6 mouse embryos at E9.5 (~7.1 mm2), E10.5 (~11.5 mm2), E11.5 (~18.8 mm2), E12.5 (~32.1 mm2), E13.5 (~48.4 mm2), E14.5 (~64.1 mm2), E15.5 (~70.8 mm2) and E16.5 (~76.1 mm2) using Stereo-seq. For E9.5-E15.5 stages, four to six sections were included from different replicates. As for E16.5, 17 sagittal sections were profiled from two biological replicates, with 13 sections from one single embryo, allowing coverage of all major organs/tissues. In the MOSTA, we provide the spatial map showing the gene expression, gene co-expression modules and regulons in each embryo sagittal sections. Our panoramic atlas will allow in-depth investigation of longstanding questions concerning mammalian development.

Axolotl Regenerative Telencephalon Interpretation via Spatiotemporal Transcriptomic Atlas (ARTISTA) is a spatially resolved transcriptomic data resource that provides visualization of gene expression across the regeneration and development stages of axolotl telencephalon at single cell resolution, aiming to provide a systematic dissection of the molecular events underlying neural regeneration in the axolotl brain, laying the foundation for further mechanistic studies. To comprehensively understand cellular dynamics occurred during axolotl brain regeneration and development, here, we carried out a series of spatial transcriptome analyses on serial sections along the rostral-caudal axis of 2 (3 sections), 5 (3 sections), 10 (3 sections), 15 (4 sections), 20 (3 sections), 30 and 60 days post injury (DPI) brain tissues after removal of a reproducible portion of dorsal pallium in left telencephalic hemisphere of 11 cm length axolotl. We also collected sections from developmental (stage 44, 54, and 57), juvenile, adult, and metamorphosed axolotl telencephalons. Based on this dataset, researchers can quickly explore the gene expression profiles of their interested cell types in spatial map across different regeneration and development stages of axolotl telencephalon.

Non-human primates provide a unique way to study the only model in which both developmental and pathological features of the brain in a species phylogenetically close to human. In the past decade, breakthrough advances in single-cell sequencing have enabled the mapping of cell taxonomy and heterogeneity in the developing and adult brain of different mammalian species. Here, we generated single-cell chromatin accessibility (single-cell ATAC) and transcriptomic data of 358,237 cells from three cortical regions of the adult cynomolgus monkey Macaca fascicularis brain. We then integrated this dataset with Stereo-seq (Spatio-Temporal Enhanced Resolution Omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular and regulatory states.

Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell fate decisions. Here, we employed Stereo-seq to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 152,977 spots at a resolution of 10x10x15 µm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell fate transitions and molecular changes during zebrafish embryogenesis. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

This database is intended to curate 3D spatial transcriptomes of all stages of Drosophila embryos and larvae generated by Stereo-seq. For currently available data, Drosophila melanogaster strain w1118 embryos were collected at two late stages (14-16 h and 16-18 h after egg laying, corresponding to stage 16~17 of embryogenesis) and all three stages were also collected. These samples were subject to cryosection to generate 7~10 μm thick slices. All slices of each sample were applied to Stereo-seq chips to capture their 2D spatial transcriptomes. All the 2D spatial transcriptomes of each sample were combined to recreate their 3D spatial transcriptomes. More samples of different stages will be added in the future. With these data, one could visualize and analyze spatial expression patterns of genes of interest, 3D reconstruct tissue-specific spatial transcriptomes by clustering and annotation, simulate tissue developmental trajectory across development, identify cell signalling pathways and gene regulatory networks, examine gene functions in their intact spatial context, etc.

We present the first in situ single-cell transcriptome profiling in plant, scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing), which enabled the bona fide single-cell spatial transcriptome of Arabidopsis leaves.

This website offers an open and interactive database for interrogation of snRNA-seq dataset and stereo-seq maps in macaque hypothalamus. Its comprehensive single-cell transcriptomic atlas provides valuable insights into the molecular changes of individual cells in various hypothalamic regions in control, obese and type 2 diabetic macaques. As a result, researchers studying metabolic disorders such as diabetes and obesity can use this resource to enhance their understanding of the molecular mechanisms that underlie such conditions.

The liver is one of the largest organs in mammals and performs fundamental body functions. Despite its regular histological structure, hepatic cell responses in homeostasis and perturbation are yet poorly understood. This is due to the difficulty of systematically studying the characteristics and crosstalk of multiple cell types in different cell states and locations, some of which are transient. Here, we used Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing) combined with high-throughput single-cell transcriptomic analysis to profile murine liver homeostasis and regeneration after partial resection. Our integrative analysis dissects with unprecedented resolution the transcriptomic gradients controlling liver cell function at the whole lobe scale, carefully defining how genes and gene regulatory networks are modulated through intercellular communication. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as an inflammation-induced master switch derepressing genes necessary for hepatocyte proliferation. Our work lays the foundation for future high-definition and tissue scale spatiotemporal studies of organ physiology and malfunction.

Cholestatic injuries, characterized by regional damage around the periportal region, lack curative therapies and cause considerable mortality. In this study, we generated a high-definition spatiotemporal atlas during cholestatic injury and repair by Stereo-seq and single-cell transcriptomics. We uncovered that cholangiocytes function as a periportal hub (cholangio-hub) by integrating multiple signals with neighboring cells. Feedback between cholangiocytes and lipid-associated macrophages (LAM) was detected in the cholangio-hub, which is related to the differentiation of LAM, a recently identified subpopulation of macrophages crucial in tissue injury. Moreover, the cholangio-hub highly expressed TGFβ, which is associated with cholangiocyte conversion of liver progenitor-like cells during injury and dampened proliferation of periportal hepatocytes during recovery. Importantly, spatiotemporal analysis revealed a key inhibitory rheostat for hepatocyte proliferation. Our data provide a comprehensive resource for demarcating regional cholestatic injuries.

A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging due to the lack of distinct marker genes to distinguish each cell types, particularly the various types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of developing maize ear primordia, identifying twelve cell types, including the four newly cell types that mainly distributed on inflorescence merisetm. Through integrating single-cell RNA transcriptomes, we identified a series of spatially-specific networks and hub genes, which may provide new insights on understanding the formation of different tissues. Furthermore, by extracting the meristem components for detailed clustering, we identified three subtypes of meristem, and validated two MADS-box genes specifically expressed at the apex of determinate meristems, involved in stem cell determinacy. In summary, this study provides a valuable resource for cereal inflorescence development studies, offering new clues for yield improvement.

Recent discoveries about the molecular heterogeneity of the cerebellar cortex suggest the existence of functionally divergent subclasses of anatomically defined cell types. Using spatial transcriptome and single-nucleus RNA-seq analysis, we mapped 3D transcriptomic atlases of the whole cerebellum of mice, marmosets, and macaques at the single-cell resolution. Comparative analysis revealed specific cell types, cell localizations, and intra-cerebellum molecular heterogeneity across species. A comprehensive database generated from this study will expand the acknowledgment of the mammalian cerebellum.

MPSTA database has a total of 15 sagittal sections from C57BL/6 mouse uterine at E7.5 (x2), E8.5 (x2), E9.5 (x2), E10.5 (x3), E10.5 HFD(x1), E12.5 (x2), E14.5 (x2), E14.5 HFD (x1) using Stereo-seq. For each stages, at least two sections were included. In the MPSTA, we provide the spatial map showing the gene expression and subregions annotation in each embryo sagittal sections. Our panoramic atlas will allow in-depth investigation of longstanding questions concerning placenta development.

CTSTA database has a total of 51 sections from gy14 cucumber floral bud at FM, stage 4-7, stage 8-1, stage 8-2, stage 8-3 and stage 8-4, and 12 sections from TS69 tomato floral bud at stage 6, stage 7 and stage8, using Stereo-seq. For each section has at least two biological replicated.In the CTSTA, we provide the spatial map showing the gene expression in each section of cucumber and tomato floral bud. Our panoramic atlas will allow in-depth investigation of longstanding questions concerning the development of cucumber and tomato.

The HHSTA database comprises 32 sections from the middle region of the hippocampus, obtained using Stereo-seq. From 16 samples, two biological replicates were collected per sample. In HHSTA, we present spatial maps illustrating cell distribution and gene expression for each section. This hippocampus atlas enables in-depth investigation into longstanding questions regarding the pathogenesis of Alzheimer's disease.

Soybean is an important crop to provide plant protein and oil for human beings and livestock. Revealing the spatial and temporal expression of soybean genes is critical for the understanding of its organ development. Thus, we constructed this database, Soybean Organ Transcriptomic Atlas (SOTA), to host and present the snRNA-seq and Stereo-seq data we generated for the five representative soybean organs (root, nodule, shoot apical meristem, leaf, and stem). SOTA provides download access to the data, online presentation and exploration of the cell clustering and annotation results of both the single cell/nucleus sequencing data and the spatial transcriptome sequencing data, as well as 3D models of root and nodule with gene expression to be shown in spatial positions. This database can facilitate exploring gene expressions and cell types, making it a valuable resource for accelerating future soybean research and breeding.

Adult zebrafish robustly regenerate injured hearts through a complex orchestration of cells and molecules. However, the comprehensive process remains incompletely understood. Here, we utilized single-cell RNA-sequencing (scRNA-seq) and Stereo-seq approaches to generate a spatially-resolved cell dataset of regenerating zebrafish heart. We captured organ-scale cellular dynamics across eight time points, with a particular focus on the initiative stages. We reconstructed a 4D "virtual regenerating heart" atlas, encompassing 3 spatial dimensions and time, comprising a total of 569,896 cells/spots derived from 36 scRNA-seq libraries and 224 Stereo-seq slices.

The ABSNA database collected single-cell maps of complete amniotic animal brains from five species. Among them, Chinese softshell turtles (Pelodiscus sinensis), zebra finches (Taeniopygia guttata) and pigeon (Columba livia) were sequenced using BGI's C4 platform. The dataset integrates and compares the brain maps of these three species with those of mice and macaques that have been studied.

Flysta3D is an extensive multi-omics atlas that encompasses the developmental life span of Drosophila, from embryonic to pupal stages. The datasets included in this atlas feature 3D single-cell spatial transcriptomics, single-cell transcriptomics, and single-cell chromatin accessibility profiles. By constructing trajectories of cell states, Flysta3D unveils the intricate regulatory mechanisms governing tissue development. Offering an unprecedented wealth of resources, Flysta3D propels research into Drosophila development by providing integrated multi-omics data at an ultra-high spatial and temporal resolution.

Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells.

The primate brain exhibits complex cellular and connectomic organization that remains elusive. Here, we present a three-dimensional multi-omic atlas of the marmoset brain, integrating single-cell spatial transcriptomics with multi-modal neuroimaging and connectomics. Our analysis reveals that cortical organization is shaped by opposing molecular gradients emanating from allocortical and primary sensory regions and converging in association cortices, reconciling competing hypotheses of cortical expansion. This gradient underlies gradual and abrupt transcriptomic transitions defining cortical boundaries and aligns with molecular architecture in the thalamus and striatum, reflecting coordinated cortico-subcortical interactions. The marmosetdefault mode-like network, positioned at the apex of gradient convergence, exhibits the most complex molecular identity, with the frontal pole sharing transcriptomic, but not connectomic, features of this network. Notably, cross-species analysis highlights shared molecular specializations in human and marmoset auditory cortices, suggesting convergent evolution for complex vocal communication. This integrative resource provides fundamental insights into primate cortical organization, specialization, and evolution.